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The first settlements in Regensburg date to the Stone Age. The Celtic name Radasbona was the oldest name given to a settlement near the present city. Around AD 90 the Romans built a small "cohort-fort" in what would now be the suburbs.

In 179 the Roman fort Castra Regina ("fortress by the river Regen") was built for Legio III Italica during the reign of Emperor Marcus Aurelius.[2] It was an important camp on the most northern point of the Danube: it corresponds to what is today the core of Regensburg's Altstadt ("Old City") east of the Obere and Untere Bachgasse and West of the Schwanenplatz. It is believed that even in late Roman times it was the seat of a bishop, and St Boniface re-established the Bishopric of Regensburg in 739.

From the early 6th century, Regensburg was the seat of the Agilolfing ruling family. From about 530 to the first half of the 13th century, it was the capital of Bavaria.
Regensburg remained an important city during the reign of Charlemagne. In 792, Regensburg hosted the ecclesiatical section of Charlemagne's General Assembly. The bishops in council condemned the heresy of Adoptionism taught by the Spanish bishops, Elipandus of Toledo and Felix of Urgel. After the partition of the Carolingian Empire, the city became the seat of the Eastern Frankish ruler, Louis II the German in 843. About two years later, in 845, fourteen Bohemian princes came to Regensburg to receive baptism there. This was the starting point of Christianization of the Czech people, and the diocese of Regensburg became the mother diocese of Prague. These events had a wide impact on the cultural history of the Czech lands, as they were consequently incorporated into the Roman Catholic and not into the Slavic-Orthodox world. The fact is well remembered, and a memorial plate at St John's Church (the alleged place of the baptism) was unveiled a few years ago, commemorating the incident in the Czech and German languages.

In 1096, on the way to the First Crusade, Peter the Hermit led a mob of Crusaders who attempted to force the mass conversion of the Jews of Regensburg and killed all those who resisted.[3]

In 1135–1146 a bridge across the Danube, the Steinerne Brücke, was built. This stone bridge opened major international trade routes between Northern Europe and Venice, and this started Regensburg's golden age as a city of wealthy trading families. Regensburg became the cultural centre of southern Germany and was celebrated for its gold work and fabrics.

The city adopted the Protestant Reformation in 1542, and its Town Council remained entirely Lutheran until the incorporation of the city into the Principality of Regensburg under Carl von Dalberg in 1803. A minority of the population remained Roman Catholic and Roman Catholics were denied civil rights ("Bürgerrecht"). The town of Regensburg must not be confused with the Bishopric of Regensburg. Although the Imperial city had adopted the Reformation, the town remained the seat of a Roman Catholic bishop and several abbeys. Three of the latter, St. Emmeram, Niedermünster and Obermünster, were estates of their own within the Holy Roman Empire, meaning that they were granted a seat and a vote at the Imperial diet (Reichstag). So there was the unique situation that the town of Regensburg comprised five independent "states" (in terms of the Holy Roman Empire): the Protestant city itself, the Roman Catholic bishopric and the three monasteries mentioned above.

From 1663 to 1806, the city was the permanent seat of the Reichstag of the Holy Roman Empire. Thus Regensburg was one of the central towns of the Empire, attracting visitors in large numbers. In 1803 the city lost its status as a free city. It was handed over to the Archbishop of Mainz and Archchancellor of the Holy Roman Empire Carl von Dalberg in compensation for Mainz, which had become French under the terms of the Treaty of Lunéville in 1801. The archbishopric of Mainz was formally transferred to Regensburg. Dalberg united the bishopric, the monsteries and the town itself, making up the Principality of Regensburg (Fürstentum Regensburg). Dalberg strictly modernised public life. Most importantly he awarded equal rights to Protestants and Roman Catholics alike. In 1810 Dalberg ceded Regensburg to the Kingdom of Bavaria, he himself being compensated by the towns of Fulda and Hanau being given to him under the title of "Grand Duke of Frankfurt".

Between April 19 and April 23, 1809, Regensburg was the scene of the Battle of Ratisbon between forces commanded by Baron de Coutaud (the 65th Ligne) and retreating Austrian forces. It was eventually overrun after supplies and ammunition ran out. The city suffered severe damage during the fight with about 150 houses being burnt and others being looted.

The Dom (Cathedral) is a very interesting example of pure German Gothic and counts as the main work of Gothic architecture in Bavaria. It was founded in 1275 and completed in 1634, with the exception of the towers, which were finished in 1869. The interior contains numerous interesting monuments, including one of Peter Vischer's masterpieces. Adjoining the cloisters are two chapels of earlier date than the cathedral itself, one of which, known as the old cathedral, goes back perhaps to the 8th century. The official choir for the liturgical music at St Peter's Cathedral are the famous Regensburger Domspatzen.

The Stone Bridge, built 1135–1146, is a highlight of medieval bridge building. The knights of the 2nd and 3rd crusade used it to cross the Danube on their way to the Holy Land.

Remains of the Roman fortress' walls including the Porta Praetoria.

The Church of St. James, also called Schottenkirche, a Romanesque basilica of the 12th century, derives its name from the monastery of IrishBenedictines (Scoti) to which it was attached; the principal doorway is covered with very singular grotesque carvings. It stands next to the Jakobstor, a mediæval city gate named after it.

The old parish church of St. Ulrich is a good example of the Transition style of the 13th century, and contains a valuable antiquarian collection. It houses the diocesan museum for religious art.

Examples of the Romanesque basilica style are the church of Obermünster, dating from 1010, and the abbey church of St. Emmeram, built in the 13th century, remarkable as one of the few German churches with a detached bell tower. The beautiful cloisters of the ancient abbey, one of the oldest in Germany, are still in a fair state of preservation. In 1809 the conventual buildings were converted into a palace for the prince of Thurn and Taxis, hereditary postmaster-general of the Holy Roman Empire.

The Adler-Apotheke, located nearby the Regensburg Cathedral, was founded in 1610 and is one of the oldest Pharmacies in Regensburg. Even today you can take a look at the ancient interior and historical vessels.

Wealthy patrician families competed against each other to see who would be able to build the highest tower of the city. In 1260, the Goldener Turm (golden tower) was built on Wahlenstraße.

The Town Hall, dating in part from the 14th century, contains the rooms occupied by the Imperial diet from 1663 to 1806.

A historical interest is also attached to the Gasthof zum Goldenen Kreuz (Golden Cross Inn), where Charles V made the acquaintance of Barbara Blomberg, the mother of Don John of Austria (born 1547).

Perhaps the most pleasant modern building in the city is the Gothic villa of the king of Bavaria on the bank of the Danube.

St. Emmeram's Abbey, now known as Schloss Thurn und Taxis, is a huge castle owned by the powerful Thurn and Taxis family.

Near Regensburg there are two very imposing Classical buildings, erected by Ludwig I of Bavaria as national monuments to German patriotism and greatness. The more imposing of the two is the Walhalla, a costly reproduction of the Parthenon, erected as a Teutonic temple of fame on a hill rising from the Danube at Donaustauf, 15 km to the east. The interior, which is as rich as coloured marble, gilding, and sculptures can make it, contains the busts of more than a hundred German worthies. The second of King Ludwig's buildings is the Befreiungshalle at Kelheim, 30 km above Regensburg, a large circular building which has for its aim the glorification of the heroes of the 1813 War of Liberation.

BMW operates an automobile production plant in Regensburg; the Regensburg BMW plant produces 3-series and 1-series vehicles. Other major employers are Siemens with its subsidiary Osram Opto-Semiconductors and Siemens VDO (now Continental AG) with the headquarters of its car component business. Infineon, the former Siemens semiconductor branch, has a medium-sized factory in Regensburg. Other well known companies such as Maschinenfabrik Reinhausen, Toshiba or Krones have built plants in or near Regensburg. Amazon has also located its German customer service centre in Regensburg.

The University of Regensburg and trading also play a major role in Regensburg's economy. Some Hightech-Biotech Companies were also founded in Regensburg and have their headquarters and laboratories in the "BioPark".

Pope Benedict XVI (professor of theology at the University of Regensburg from 1969 to 1977, and still classed as honorary professor; he was never a resident of the city of Regensburg, however his house in Pentling lies less than 1 kilometer from the city in the district of Regensburg, and he has been an honorary citizen since 2006)